The LAILAPS Search Engine: Relevance Ranking in Life Science Databases

The German Federal ex situ Genebank of Agricultural and Horticultural Crop Species is the largest collection of its kind in the countries of the European Union and amongst the 10 largest collections worldwide. Beside its enormous scientific value as a safeguard of plant biodiversity, the plant genetic resources maintained are also of high importance for breeders to provide new impulses. The complex processes of managing such a collection are supported by the Genebank Information System (GBIS). GBIS is an important source of information for researchers and plant breeders, e.g. for identifying appropriate germplasm for breeding purposes. In addition, the access to genebank material as a sovereign task is also of high interest to the general public. Moreover, GBIS acts as a data source for global information systems, such as the Global Biodiversity Information Facility (GBIF) or the European Search Catalogue for Plant Genetic Resources (EURISCO).Database URL: http://gbis.ipk-gatersleben.de/

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LAILAPS: The Plant Science Search Engine

Esch

Chen

Colmsee

et al. 2014

Plant and Cell Physiology

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With the number of sequenced plant genomes growing, the number of predicted genes and functional annotations is also increasing. The association between genes and phenotypic traits is currently of great interest. Unfortunately, the information available today is widely scattered over a number of different databases. Information retrieval (IR) has become an all-encompassing bioinformatics methodology for extracting knowledge from complex, heterogeneous and distributed databases, and therefore can be a useful tool for obtaining a comprehensive view of plant genomics, from genes to traits. Here we describe LAILAPS (http://lailaps.ipk-gatersleben.de), an IR system designed to link plant genomic data in the context of phenotypic attributes for a detailed forward genetic research. LAILAPS comprises around 65 million indexed documents, encompassing >13 major life science databases with around 80 million links to plant genomic resources. The LAILAPS search engine allows fuzzy querying for candidate genes linked to specific traits over a loosely integrated system of indexed and interlinked genome databases. Query assistance and an evidence-based annotation system enable time-efficient and comprehensive information retrieval. An artificial neural network incorporating user feedback and behavior tracking allows relevance sorting of results. We fully describe LAILAPS’s functionality and capabilities by comparing this system’s performance with other widely used systems and by reporting both a validation in maize and a knowledge discovery use-case focusing on candidate genes in barley.

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The LAILAPS Search Engine: Relevance Ranking in Life Science Databases

Cited by 6 publications

References 13 publications

Information Retrieval in Life Sciences: A Programmatic Survey

Information Retrieval in Life Sciences: A Programmatic Survey

GBIS: the information system of the German Genebank

LAILAPS: The Plant Science Search Engine

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